The filter is a 52mm Hoya 10 stops it is screwed on the lensI need to try the 28-70 kit lens with nd filter but I'm away right now.

What surprises me is the sharp edge at the bottom, fading a bit towards the top of the frame. Seems like something is going on close to the sensor rather than in front of the lens.

I think the same. I mean if it happens in portrait but not landscape it has to be something mechanical. Maybe the shutter is still a bit there with the long eposure times? Maybe it's a mechanical shutter problem.